I did a engine swap & the same thing happened to me.The #4 ground wire on mine had a loose connection causing the same problem. Check the harness between the intake manifold & the fender. Chances are when you moved the harness you loosened or broke the connection. Remove the wire loom (wire cover) & there are 2 white wires with a red strip, those are the ground wires for the injectors. Each one then splits into 2 giving you 4 wires for your injectors. You can do this with out removing the upper intake. 

If you don't find the problem there you'll have to check further & remove the upper intake